At least 38 people are dead and 50 are missing after record-shattering torrential rains hit western and central Japan on Saturday.
Although a weather front had settled between western and eastern Japan, there was a risk heavy rains would continue as warm air flowed towards the front, it added, with already-saturated areas facing more rain on Sunday.
According to the Kyodo news agency, one person died in a landslide in Hiroshima, which had set off a fire. On Nuwa Island, off the prefectural capital of Matsuyama, a woman in her 30s and her two children were killed when a mudslide hit their home.
Heavy rainfall had damaged at least 500 houses and injured 40 people by 7 am local time (3.30 am Indian Standard Time) on Saturday, The Japan Times reported.
In the prefectural capital of Hiroshima, a vehicle with a mother with her three children was swept away by flood waters in the city's Aki Ward.
Intense rainfall triggered huge landslides and flash floods in Hiroshima, Okayama, Kyoto and other regions, while hampering rescue operations.
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As the weather agency only issues such warnings when it anticipates extreme conditions that could result in major disasters that only occur once or twice in a half-century, the issuance of the special warnings suggests people should remain on high alert and take shelter if necessary.
Hiroshima Prefecture was hit the hardest by landslides that claimed 22 lives, while 18 died in Ehime Prefecture, with others killed in Osaka, Shiga, Hyogo, Okayama, Yamaguchi and Fukuoka prefectures.
Video from Okayama showed brown water engulfing residential areas with some people fleeing to rooftops and balconies, trying to catch the attention of hovering rescue helicopters.
A woman who had gone missing after leaving her home in Kameoka, Kyoto Prefecture, in her vehicle was found dead in a river in Nose, Osaka Prefecture, on Friday.
Mitsubishi Motors Corp said it had halted operations at its Okayama Prefecture plant as it was unable to procure parts, while Daihatsu said it had suspended production at two plants in Osaka and Kyoto for the same reason. "In fear of heavier downpours, we've issued emergency warnings in areas where the amount of rain hasn't exceeded the standards of such a warning system", a JMA official explained.
Prime Minister Shinzo Abe warned "the situation is extremely serious" and ordered his government to "make an all-out effort" to rescue those affected.